Article
Biochemistry & Molecular Biology
Minh Ngoc Le, Cong Truc Le, Tuan Anh Nguyen
Summary: This article introduces a new method, intramolecular ligation method (iLIME), for quantifying and sequencing hairpin-containing pre-miRNAs. The method converts pre-miRNAs into circularized RNAs using T4 RNA ligase 1, allowing for PCR primer design for quantification and next-generation sequencing for end sequencing. This method offers a simple and effective solution for studying pre-miRNAs.
Article
Biochemical Research Methods
Ravil R. Garafutdinov, Guzel F. Burkhanova, Igor V. Maksimov, Assol R. Sakhabutdinova
Summary: In this study, a new isothermal amplification method called multimerization was developed for the detection of specific mature miRNA. This technique is simple, versatile, and does not require a reverse transcription step or additional stem-loop or fluoro-genic probes. It can accurately exclude pri-or pre-miRNA from analysis and has been successfully applied to the detection of Tae-miRNA159 in wheat plants affected by Stagonospora nodorum Berk infection.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Chemistry, Analytical
Jian Wei, Yuanyuan Zhang, Shengjuan Liu, Jinwen Zhao, Ruo Yuan, Shihong Chen
Summary: This study presents a CRISPR/Cas12a-based fluorescence system using carboxyl-functionalized poly[9,9-bis(3 '-(N,N-dimethylamino)propyl)-2,7-fluorene]-alt-2,7-(9,9-dioctylfluorene)] nanoparticles (c-PFN NPs) as fluorescence donor and Au-polydopamine-Au nanoparticles (Au-PDA-Au NPs) as fluorescent acceptor. Magnetic bead-assisted high-efficiency DNA nanocarrier (MHDN) is introduced to reduce interference and background signal. The system achieves high sensitivity for miRNA-155 detection through multi-sited rolling circle amplification and enzymatic cleavage of quenching probes.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Biochemistry & Molecular Biology
Margarita Kniazeva, Lidia Zabegina, Andrey Shalaev, Olga Smirnova, Olga Lavrinovich, Igor Berlev, Anastasia Malek
Summary: Cervical cancer is a common gynecological malignancy that can be prevented through yearly diagnosis and treatment of pre-cancerous cervical disease. The NOVAprep-miR-CERVIX is a new method that assesses cervical dysplasia by analyzing six marker miRNAs. This study aims to evaluate the performance and diagnostic potency of this new approach.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mai Ngoc Hoang, Clemens Peterbauer
Summary: Lactococcus lactis can be used as a drug delivery vector by displaying recombinant proteins on its surface, enabling painless administration and triggering robust immune response. A double-labeling method using specific dyes allows simultaneous detection and quantification of targeted proteins on the cell surface and in the cytoplasm, providing a convenient tool for monitoring the processes for cell surface display applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Jeonghun Kim, So Yeon Ahn, Soong Ho Um
Summary: This study presents a novel DNA nanostructure for detecting cancer miRNA variants with temperature insensitivity and high selectivity. By optimizing parameters and considering thermodynamic stability, design guidelines for new sensing systems of miRNA variation were provided.
Article
Chemistry, Multidisciplinary
Zihan Zhong, Shu Lv, Kaibo Shi
Summary: This paper proposes a new framework for time-series event prediction, which transforms the prediction problem into a labeling problem to capture the timing relationship between subsequence sets. The framework utilizes a sequence clustering algorithm to identify representative patterns, and uses XGBoost for feature selection. The preliminary prediction value is obtained using LSTM, and further refined using CRF. Experimental results show that this method improves prediction accuracy compared to other models.
APPLIED SCIENCES-BASEL
(2023)
Article
Spectroscopy
Paramita Saha, Murali Monohar Pandey
Summary: A new fluorescence-based method for estimating rotigotine in bulk and nanoformulations has been developed and validated. The method demonstrates good linearity and accuracy, and is specific and robust for use in pharmaceutical dosage forms.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Analytical
Yunfei Guo, Jun Li, Hao Yang, Hongchen Gu, Gaolian Xu, Hong Xu
Summary: STEM-Mi-PCR is a multiplexed miRNA detection method that allows for simultaneous detection of multiple miRNAs with high sensitivity and specificity. It can also discriminate single nucleotide mutations in miRNAs. This method holds promise for future clinical applications in miRNA profiling.
Article
Biology
Shigeyuki Shichino, Satoshi Ueha, Shinichi Hashimoto, Tatsuro Ogawa, Hiroyasu Aoki, Bin Wu, Chang-Yu Chen, Masahiro Kitabatake, Noriko Ouji-Sageshima, Noriyoshi Sawabata, Takeshi Kawaguchi, Toshitugu Okayama, Eiji Sugihara, Shigeto Hontsu, Toshihiro Ito, Yasunori Iwata, Takashi Wada, Kazuho Ikeo, Taka-Aki Sato, Kouji Matsushima
Summary: Terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) is a method for single-cell RNA sequencing that improves the generation of libraries. It has significant implications in the analysis of cellular heterogeneity and cell-cell interaction networks.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xiao-Yu Wang, Chun-Jing Chen, Yao-Hui He, Lian-Shuai Ding, Yi-Fan Wu, Cheng-Ting Huang, Jun Wu, Rong Ding, Yu-Hua Xue, Zhi-Wei Lin, Peng-Xiang Xu, Yi-Le Wu, Wen Liu, Ji-Jun Li, Si-Ming Chen, Yu-Fen Zhao, Ji-Yang Dong, Qiang Zhou, Xiang Gao
Summary: Stable isotope chemical labeling methods have limitations in high sensitivity detection for quantitative proteomics. A novel isobaric stable isotope N-phosphorylation labeling strategy (iSIPL) was developed for precise quantitative proteome analysis with high sensitivity and accuracy. iSIPL strategy was successfully applied to analyze the dynamics of protein-protein interactions in the transactivation of HIV-1 provirus.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Zhen Gao, Yu-Tian Wang, Qing-Wen Wu, Lei Li, Jian-Cheng Ni, Chun-Hou Zheng
Summary: This paper proposes a novel method based on matrix completion and non-negative matrix factorization (MCNMF) for predicting disease-associated miRNAs. Experimental results demonstrate the effectiveness and reliability of the proposed method.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Nadezhda Nikiforova, Maria Chumachenko, Inga Nazarova, Lidia Zabegina, Maria Slyusarenko, Elena Sidina, Anastasia Malek
Summary: The quantification of disease-associated populations of circulating extracellular membrane nanovesicles (ENVs) has opened new opportunities for liquid biopsy, but the sensitivity is still not optimal for routine clinical application. This study developed a new approach to non-specific ENV staining and SEC fractionation to increase the sensitivity of bead-assisted flow cytometry. The process of CM-Dil-stained plasma fractionation was characterized in detail, and the fractions with optimal characteristics were identified, while also exploring the sensitivity of on-bead flow cytometry for specific populations of plasma ENVs and demonstrating the advantages and limitations of the technique.
Article
Medicine, General & Internal
Shiyuan Gao, Zhufang Kuang, Tao Duan, Lei Deng
Summary: MiRNAs play a crucial role in the study of complex human diseases. Traditional methods are limited by small sample size and high cost, so computational simulations are needed for predicting the correlation between miRNAs and diseases. This paper proposes a GCN-based DEJKMDR model that integrates biomolecular information to predict miRNA-disease associations. The model uses DropEdge and JK-Net to minimize overfitting and combine different domain scopes. Experimental results show that the model achieves higher accuracy and reliability in predicting unknown miRNA-disease relationships.
FRONTIERS IN MEDICINE
(2023)
Article
Engineering, Chemical
Hua Li, Yan Gao, Yuyuan Zhao
Summary: The study found that the expansion of silica-gel beads is caused by high pressure steam generated from water confined in the nano-pores. This finding will help to control the pore structure manufactured by the silica-gel bead infiltration method more precisely.
Article
Genetics & Heredity
Flavia Hoering, Alberto Biscontin, Lars Harms, Gabriele Sales, Christian S. Reiss, Cristiano De Pitta, Bettina Meyer
Summary: Antarctic krill exhibit seasonal differences in gene expression across different latitudinal regions, with most genes up-regulated in summer krill. The South Georgia region shows less pronounced seasonal differences, possibly due to milder conditions at lower latitudes. Krill in the South Orkneys/Bransfield Strait and Lazarev Sea regions enter a state of metabolic depression and regressed development in winter, driven by a photoperiodic timing system.
Article
Biology
Alberto Biscontin, Lisa Zarantonello, Antonella Russo, Rodolfo Costa, Sara Montagnese
Summary: The study aimed to develop a Polygenic Score-based model for molecular chronotype assessment and identified 83 variants predictive of chronotype with an estimated validity of approximately 80%.
JOURNAL OF BIOLOGICAL RHYTHMS
(2022)
Review
Cell Biology
Davide Colaianni, Cristiano De Pitta
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate protein-coding gene expression post-transcriptionally. They play important roles in the development and function of the fruit fly brain.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Francesca Grespi, Caterina Vianello, Stefano Cagnin, Marta Giacomello, Agnese De Mario
Summary: Gliomas are heterogeneous neoplasms with different malignancies and molecular hallmarks. Glioblastoma (GB) is the highest grade of glioma and its clinical outcome is poor. Recent studies show that the reshaping of the cytoskeleton and the extent and function of mitochondria-ER contact sites (MERCs) are associated with GB progression. A meta-analysis comparing different grade GB patients reveals alterations in cytoskeletal and MERCs related genes in high-grade GB. Further analysis may provide new insights into the molecular etiopathogenesis of GB and identify potential biomarkers/targets for improved therapy.
Article
Biochemistry & Molecular Biology
Lu Chen, Caitlin M. Roake, Paolo Maccallini, Francesca Bavasso, Roozbeh Dehghannasiri, Pamela Santonicola, Natalia Mendoza-Ferreira, Livia Scatolini, Ludovico Rizzuti, Alessandro Esposito, Ivan Gallotta, Sofia Francia, Stefano Cacchione, Alessandra Galati, Valeria Palumbo, Marie A. Kobin, Gian Gaetano Tartaglia, Alessio Colantoni, Gabriele Proietti, Yunming Wu, Matthias Hammerschmidt, Cristiano De Pitta, Gabriele Sales, Julia Salzman, Livio Pellizzoni, Brunhilde Wirth, Elia Di Schiavi, Maurizio Gatti, Steven E. Artandi, Grazia D. Raffa
Summary: This study identifies a neuroprotective role for TGS1 and highlights the impact of defective snRNA maturation on neuronal viability and function.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Ilenia Urso, Alberto Biscontin, Davide Corso, Cristiano Bertolucci, Chiara Romualdi, Cristiano De Pitta, Bettina Meyer, Gabriele Sales
Summary: The krill species Euphausia superba plays a critical role in the Antarctic ecosystem, but climate changes have already affected its distribution and reproductive dynamics. In this study, we identified genes involved in the krill moulting cycle, reproductive process, and sexual maturation, and discovered previously unknown differentially expressed genes related to cuticle development and energy storage. We also expanded our knowledge of the krill opsin repertoire by finding new opsin sequences. Furthermore, we created the KrillDB(2) database, which provides comprehensive information on krill genes, expression profiles, and differential expression.
SCIENTIFIC REPORTS
(2022)
Article
Environmental Sciences
Svenja J. Mueller, Katharina Michael, Ilenia Urso, Gabriele Sales, Cristiano De Pitta, Lavinia Suberg, Wiebke Wessels, Evgeny A. Pakhomov, Bettina Meyer
Summary: The pelagic tunicate Salpa thompsoni is an important metazoan grazer in the Southern Ocean, and its biomass and distribution have been positively correlated with ocean warming and winter sea ice decline. However, our understanding of the adaptation of S. thompsoni to the extreme seasonality of the Southern Ocean and the differences between its reproductive forms is limited.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Cell Biology
Stefano Cagnin, Marco Brugnaro, Caterina Millino, Beniamina Pacchioni, Carmen Troiano, Moises Di Sante, Nina Kaludercic
Summary: This study reveals the link between MAO activity, transcriptomic changes, and activation of pro-survival signaling and autophagy in diabetic cardiomyopathy.
Article
Biology
A. Porrazzo, F. Cipressa, A. De Gregorio, C. De Pitta, G. Sales, L. Ciapponi, P. Morciano, G. Esposito, M. A. Tabocchini, G. Cenci
Summary: Chronic low-dose radiation exposure reduces chromosome breaks and telomere dysfunction caused by high-dose irradiation in Drosophila cells. This protective response is associated with the downregulation of the Loquacious D gene, which is involved in esiRNA biogenesis. Loss of Loquacious D mimics the protective effect of low-dose radiation, suggesting its importance in the cellular response to radiation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
Matteo Astone, Roxana E. Oberkersch, Giovanni Tosi, Alberto Biscontin, Massimo M. Santoro
Summary: This study demonstrates that endothelial cells possess an endogenous circadian clock, and core clock genes exhibit robust circadian oscillations. Impairing the function of the circadian clock transcriptional activator BMAL1 leads to angiogenesis defects in both developmental and pathological contexts. BMAL1 regulates endothelial cell cycle progression by binding to the promoters of CCNA1 and CDK1 genes.
CARDIOVASCULAR RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Changwei Shao, Shuai Sun, Kaiqiang Liu, Jiahao Wang, Shuo Li, Qun Liu, Bruce E. Deagle, Inge Seim, Alberto Biscontin, Qian Wang, Xin Liu, So Kawaguchi, Yalin Liu, Simon Jarman, Yue Wang, Hong-Yan Wang, Guodong Huang, Jiang Hu, Bo Feng, Cristiano De Pitta, Shanshan Liu, Rui Wang, Kailong Ma, Yiping Ying, Gabrielle Sales, Tao Sun, Xinliang Wang, Yaolei Zhang, Yunxia Zhao, Shanshan Pan, Xiancai Hao, Yang Wang, Jiakun Xu, Bowen Yue, Yanxu Sun, He Zhang, Mengyang Xu, Yuyan Liu, Xiaodong Jia, Jiancheng Zhu, Shufang Liu, Jue Ruan, Guojie Zhang, Huanming Yang, Xun Xu, Jun Wang, Xianyong Zhao, Bettina Meyer, Guangyi Fan
Summary: This study reveals the molecular architecture and adaptations of the Antarctic krill genome, as well as the population dynamics associated with climate change events. The findings provide valuable insights into the genetic basis of Antarctic krill's ability to survive in the Southern Ocean and offer resources for future Antarctic research.
Article
Immunology
Lorenzo Lupi, Anna Bordin, Gabriele Sales, Davide Colaianni, Adriana Vitiello, Alberto Biscontin, Alberto Reale, Alfredo Garzino-Demo, Angelo Antonini, Giancarlo Ottaviano, Carla Mucignat, Cristina Parolin, Arianna Calistri, Cristiano De Pitta
Summary: COVID-19 is a respiratory syndrome that can cause various symptoms, including deficits in smell and taste. Transcriptome analysis of olfactory mucosa revealed altered gene expression levels in patients with persistent olfactory deficits, with associations with inflammatory response and zinc homeostasis.
FRONTIERS IN IMMUNOLOGY
(2023)
Meeting Abstract
Gastroenterology & Hepatology
Chiara Mangini, Chiara Formentin, Alberto Biscontin, Gianluca Giusti, Paolo Angeli, Lisa Zarantonello, Sara Montagnese
JOURNAL OF HEPATOLOGY
(2022)